ABSTRACT

We report here the draft whole-genome sequences for 18 Flavobacterium species type strains that have historically been associated with fish gill disease.

GENOME ANNOUNCEMENT

Bacterial gill disease (BGD) is an important disease of cultured fish worldwide. Flavobacterium branchiophilum has been identified as the causative agent of BGD (1); however, other bacteria are reported to be involved in Flavobacteriaceae-associated and nontypical bacterial gill disease (2–4). We sequenced the species in this report based on their prior association with gill disease (3) in order to facilitate investigation of the etiologic agents of bacterial gill disease in the United States.

Flavobacterium species type strains were obtained from the following repositories: the American Type Culture Collection, USA (ATCC); the Culture Collection, University of Göteborg, Sweden (CCUG); and the Leibniz Institute–German Collection of Microorganisms and Cell Cultures (DSM). DNA was extracted from Flavobacterium spp. using an UltraClean microbial DNA isolation kit (Mo Bio Laboratories, Inc., Carlsbad, CA, USA) according to the manufacturer’s recommendations. Whole-genome sequencing (WGS) was performed using V3 chemistry with paired-end 2 × 300-bp reads on the MiSeq platform (Illumina, San Diego, CA, USA). Sequencing libraries were prepared according to the Illumina Nextera XT sample preparation guide.

WGS data were imported into CLC Genomics Workbench, and a de novo assembly was performed using default CLC Genomics Workbench version 8.0 assembly parameters (Qiagen, Valencia, CA, USA). Contigs of less than 300 bp were removed from analysis. The genomes were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP version 4) (https://www.ncbi.nlm.nih.gov/genome/annotation_prok). Assemblies had between 20 and 241 contigs, between 2,638,051 and 6,041,815 bases, between 30.5% and 35.7% G+C contents, and between 2,438 and 5,164 total coding sequences (CDSs). WGS assembly data are shown in Table 1. The publicly available resistance gene database ResFinder was used for identification of antimicrobial resistance genes, using a 90% sequence identity and 60% length minimum to identify resistance genes (5). Only 2 of the 18 Flavobacterium spp. carried acquired resistance genes. The tetracycline resistance gene (tetX; 91% sequence identity) was identified in F. plurextorum (WGS0045). F. johnsoniae (CVM 41394) was found to carry blaJOHN, a class B beta-lactamase gene. None of the remaining Flavobacterium spp. were positive for any acquired resistance genes.

Summary of analyses of type strains of Flavobacterium spp. associated with fish disease

Accession number(s).These draft genome sequences have been deposited in GenBank under the accession numbers indicated in Table 1.

ACKNOWLEDGMENTS

We thank Jonathan Sabo for technical assistance.

The views expressed in this article are those of the authors and do not necessarily reflect the official policy of the Department of Health and Human Services, the U.S. Food and Drug Administration, or the U.S. Government. Reference to any commercial materials, equipment, or process does not in any way constitute approval, endorsement, or recommendation by the Food and Drug Administration.

This work was supported by the U.S. Food and Drug Administration, Center for Veterinary Medicine.

FOOTNOTES

Received 11 July 2017.

Accepted 26 July 2017.

Published 16 November 2017.

This is a work of the U.S. Government and is not subject to copyright protection in the United States. Foreign copyrights may apply.